In this work we demonstrate how to automate parts of the infectious disease-control policy-making process via performing inference in existing epidemiological models. The kind of inference tasks undertaken include computing the posterior distribution over controllable, via direct policy-making choices, simulation model parameters that give rise to acceptable disease progression outcomes. Among other things, we illustrate the use of a probabilistic programming language that automates inference in existing simulators. Neither the full capabilities of this tool for automating inference nor its utility for planning is widely disseminated at the current time. Timely gains in understanding about how such simulation-based models and inference automation tools applied in support of policymaking could lead to less economically damaging policy prescriptions, particularly during the current COVID-19 pandemic.
Probabilistic programs with mixed support (both continuous and discrete latent random variables) commonly appear in many probabilistic programming systems (PPSs). However, the existence of the discrete random variables prohibits many basic gradient-based inference engines, which makes the inference procedure on such models particularly challenging. Existing PPSs either require the user to manually marginalize out the discrete variables or to perform a composing inference by running inference separately on discrete and continuous variables. The former is infeasible in most cases whereas the latter has some fundamental shortcomings. We present a novel approach to run inference efficiently and robustly in such programs using stochastic gradient Markov Chain Monte Carlo family of algorithms. We compare our stochastic gradient-based inference algorithm against conventional baselines in several important cases of probabilistic programs with mixed support, and demonstrate that it outperforms existing composing inference baselines and works almost as well as inference in marginalized versions of the programs, but with less programming effort and at a lower computation cost.
The mixed membership stochastic blockmodel (MMSB) is a popular framework for community detection and network generation. It learns a low-rank mixed membership representation for each node across communities by exploiting the underlying graph structure. MMSB assumes that the membership distributions of the nodes are independently drawn from a Dirichlet distribution, which limits its capability to model highly correlated graph structures that exist in real-world networks. In this paper, we present a flexible richly structured MMSB model, \textit{Struct-MMSB}, that uses a recently developed statistical relational learning model, hinge-loss Markov random fields (HL-MRFs), as a structured prior to model complex dependencies among node attributes, multi-relational links, and their relationship with mixed-membership distributions. Our model is specified using a probabilistic programming templating language that uses weighted first-order logic rules, which enhances the model's interpretability. Further, our model is capable of learning latent characteristics in real-world networks via meaningful latent variables encoded as a complex combination of observed features and membership distributions. We present an expectation-maximization based inference algorithm that learns latent variables and parameters iteratively, a scalable stochastic variation of the inference algorithm, and a method to learn the weights of HL-MRF structured priors. We evaluate our model on six datasets across three different types of networks and corresponding modeling scenarios and demonstrate that our models are able to achieve an improvement of 15\% on average in test log-likelihood and faster convergence when compared to state-of-the-art network models.
Stochastic processes provide a mathematically elegant way model complex data. In theory, they provide flexible priors over function classes that can encode a wide range of interesting assumptions. In practice, however, efficient inference by optimisation or marginalisation is difficult, a problem further exacerbated with big data and high dimensional input spaces. We propose a novel variational autoencoder (VAE) called the prior encoding variational autoencoder ($\pi$VAE). The $\pi$VAE is finitely exchangeable and Kolmogorov consistent, and thus is a continuous stochastic process. We use $\pi$VAE to learn low dimensional embeddings of function classes. We show that our framework can accurately learn expressive function classes such as Gaussian processes, but also properties of functions to enable statistical inference (such as the integral of a log Gaussian process). For popular tasks, such as spatial interpolation, $\pi$VAE achieves state-of-the-art performance both in terms of accuracy and computational efficiency. Perhaps most usefully, we demonstrate that the low dimensional independently distributed latent space representation learnt provides an elegant and scalable means of performing Bayesian inference for stochastic processes within probabilistic programming languages such as Stan.
We present the preliminary high-level design and features of DynamicPPL.jl, a modular library providing a lightning-fast infrastructure for probabilistic programming. Besides a computational performance that is often close to or better than Stan, DynamicPPL provides an intuitive DSL that allows the rapid development of complex dynamic probabilistic programs. Being entirely written in Julia, a high-level dynamic programming language for numerical computing, DynamicPPL inherits a rich set of features available through the Julia ecosystem. Since DynamicPPL is a modular, stand-alone library, any probabilistic programming system written in Julia, such as Turing.jl, can use DynamicPPL to specify models and trace their model parameters. The main features of DynamicPPL are: 1) a meta-programming based DSL for specifying dynamic models using an intuitive tilde-based notation; 2) a tracing data-structure for tracking RVs in dynamic probabilistic models; 3) a rich contextual dispatch system allowing tailored behaviour during model execution; and 4) a user-friendly syntax for probabilistic queries. Finally, we show in a variety of experiments that DynamicPPL, in combination with Turing.jl, achieves computational performance that is often close to or better than Stan.
Markov chain Monte Carlo (MCMC) is widely regarded as one of the most important algorithms of the 20th century. Its guarantees of asymptotic convergence, stability, and estimator-variance bounds using only unnormalized probability functions make it indispensable to probabilistic programming. In this paper, we introduce the TensorFlow Probability MCMC toolkit, and discuss some of the considerations that motivated its design.
Stochastic variational inference offers an attractive option as a default method for differentiable probabilistic programming. However, the performance of the variational approach depends on the choice of an appropriate variational family. Here, we introduce automatic structured variational inference (ASVI), a fully automated method for constructing structured variational families, inspired by the closed-form update in conjugate Bayesian models. These convex-update families incorporate the forward pass of the input probabilistic program and can therefore capture complex statistical dependencies. Convex-update families have the same space and time complexity as the input probabilistic program and are therefore tractable for a very large family of models including both continuous and discrete variables. We validate our automatic variational method on a wide range of low- and high-dimensional inference problems. We find that ASVI provides a clear improvement in performance when compared with other popular approaches such as the mean-field approach and inverse autoregressive flows. We provide an open source implementation of ASVI in TensorFlow Probability.
A central tenet of probabilistic programming is that a model is specified exactly once in a canonical representation which is usable by inference algorithms. We describe JointDistributions, a family of declarative representations of directed graphical models in TensorFlow Probability.
Though neural network models demonstrate impressive performance, we do not understand exactly how these black-box models make individual predictions. This drawback has led to substantial research devoted to understand these models in areas such as robustness, interpretability, and generalization ability. In this paper, we consider the problem of exploring the prediction level sets of a classifier using probabilistic programming. We define a prediction level set to be the set of examples for which the predictor has the same specified prediction confidence with respect to some arbitrary data distribution. Notably, our sampling-based method does not require the classifier to be differentiable, making it compatible with arbitrary classifiers. As a specific instantiation, if we take the classifier to be a neural network and the data distribution to be that of the training data, we can obtain examples that will result in specified predictions by the neural network. We demonstrate this technique with experiments on a synthetic dataset and MNIST. Such level sets in classification may facilitate human understanding of classification behaviors.
We introduce the notion of a stochastic probabilistic program and present a reference implementation of a probabilistic programming facility supporting specification of stochastic probabilistic programs and inference in them. Stochastic probabilistic programs allow straightforward specification and efficient inference in models with nuisance parameters, noise, and nondeterminism. We give several examples of stochastic probabilistic programs, and compare the programs with corresponding deterministic probabilistic programs in terms of model specification and inference. We conclude with discussion of open research topics and related work.
NumPyro is a lightweight library that provides an alternate NumPy backend to the Pyro probabilistic programming language with the same modeling interface, language primitives and effect handling abstractions. Effect handlers allow Pyro's modeling API to be extended to NumPyro despite its being built atop a fundamentally different JAX-based functional backend. In this work, we demonstrate the power of composing Pyro's effect handlers with the program transformations that enable hardware acceleration, automatic differentiation, and vectorization in JAX. In particular, NumPyro provides an iterative formulation of the No-U-Turn Sampler (NUTS) that can be end-to-end JIT compiled, yielding an implementation that is much faster than existing alternatives in both the small and large dataset regimes.
Even as deep neural networks have become very effective for tasks in vision and perception, it remains difficult to explain and debug their behavior. In this paper, we present a programmatic and semantic approach to explaining, understanding, and debugging the correct and incorrect behaviors of a neural network-based perception system. Our approach is semantic in that it employs a high-level representation of the distribution of environment scenarios that the detector is intended to work on. It is programmatic in that scenario representation is a program in a domain-specific probabilistic programming language which can be used to generate synthetic data to test a given perception module. Our framework assesses the performance of a perception module to identify correct and incorrect detections, extracts rules from those results that semantically characterizes the correct and incorrect scenarios, and then specializes the probabilistic program with those rules in order to more precisely characterize the scenarios in which the perception module operates correctly or not. We demonstrate our results using the SCENIC probabilistic programming language and a neural network-based object detector. Our experiments show that it is possible to automatically generate compact rules that significantly increase the correct detection rate (or conversely the incorrect detection rate) of the network and can thus help with understanding and debugging its behavior.
This work presents the concept of kernel mean embedding and kernel probabilistic programming in the context of stochastic systems. We propose formulations to represent, compare, and propagate uncertainties for fairly general stochastic dynamics in a distribution-free manner. The new tools enjoy sound theory rooted in functional analysis and wide applicability as demonstrated in distinct numerical examples. The implication of this new concept is a new mode of thinking about the statistical nature of uncertainty in dynamical systems.
Bayesian inference in state-space models is challenging due to high-dimensional state trajectories. A viable approach is particle Markov chain Monte Carlo, combining MCMC and sequential Monte Carlo to form "exact approximations" to otherwise intractable MCMC methods. The performance of the approximation is limited to that of the exact method. We focus on particle Gibbs and particle Gibbs with ancestor sampling, improving their performance beyond that of the underlying Gibbs sampler (which they approximate) by marginalizing out one or more parameters. This is possible when the parameter prior is conjugate to the complete data likelihood. Marginalization yields a non-Markovian model for inference, but we show that, in contrast to the general case, this method still scales linearly in time. While marginalization can be cumbersome to implement, recent advances in probabilistic programming have enabled its automation. We demonstrate how the marginalized methods are viable as efficient inference backends in probabilistic programming, and demonstrate with examples in ecology and epidemiology.
Causal inference can be formalized as Bayesian inference that combines a prior distribution over causal models and likelihoods that account for both observations and interventions. We show that it is possible to implement this approach using a sufficiently expressive probabilistic programming language. Priors are represented using probabilistic programs that generate source code in a domain specific language. Interventions are represented using probabilistic programs that edit this source code to modify the original generative process. This approach makes it straightforward to incorporate data from atomic interventions, as well as shift interventions, variance-scaling interventions, and other interventions that modify causal structure. This approach also enables the use of general-purpose inference machinery for probabilistic programs to infer probable causal structures and parameters from data. This abstract describes a prototype of this approach in the Gen probabilistic programming language.
Universal probabilistic programming systems (PPSs) provide a powerful framework for specifying rich probabilistic models. They further attempt to automate the process of drawing inferences from these models, but doing this successfully is severely hampered by the wide range of non--standard models they can express. As a result, although one can specify complex models in a universal PPS, the provided inference engines often fall far short of what is required. In particular, we show that they produce surprisingly unsatisfactory performance for models where the support varies between executions, often doing no better than importance sampling from the prior. To address this, we introduce a new inference framework: Divide, Conquer, and Combine, which remains efficient for such models, and show how it can be implemented as an automated and generic PPS inference engine. We empirically demonstrate substantial performance improvements over existing approaches on three examples.
We present a framework for automatically structuring and training fast, approximate, deep neural surrogates of stochastic simulators. Unlike traditional approaches to surrogate modeling, our surrogates retain the interpretable structure and control flow of the reference simulator. Our surrogates target stochastic simulators where the number of random variables itself can be stochastic and potentially unbounded. Our framework further enables an automatic replacement of the reference simulator with the surrogate when undertaking amortized inference. The fidelity and speed of our surrogates allow for both faster stochastic simulation and accurate and substantially faster posterior inference. Using an illustrative yet non-trivial example we show our surrogates' ability to accurately model a probabilistic program with an unbounded number of random variables. We then proceed with an example that shows our surrogates are able to accurately model a complex structure like an unbounded stack in a program synthesis example. We further demonstrate how our surrogate modeling technique makes amortized inference in complex black-box simulators an order of magnitude faster. Specifically, we do simulator-based materials quality testing, inferring safety-critical latent internal temperature profiles of composite materials undergoing curing.
It is a significant challenge to design probabilistic programming systems that can accommodate a wide variety of inference strategies within a unified framework. Noting that the versatility of modern automatic differentiation frameworks is based in large part on the unifying concept of tensors, we describe a software abstraction for integration --functional tensors-- that captures many of the benefits of tensors, while also being able to describe continuous probability distributions. Moreover, functional tensors are a natural candidate for generalized variable elimination and parallel-scan filtering algorithms that enable parallel exact inference for a large family of tractable modeling motifs. We demonstrate the versatility of functional tensors by integrating them into the modeling frontend and inference backend of the Pyro programming language. In experiments we show that the resulting framework enables a large variety of inference strategies, including those that mix exact and approximate inference.
Naive approaches to amortized inference in probabilistic programs with unbounded loops can produce estimators with infinite variance. This is particularly true of importance sampling inference in programs that explicitly include rejection sampling as part of the user-programmed generative procedure. In this paper we develop a new and efficient amortized importance sampling estimator. We prove finite variance of our estimator and empirically demonstrate our method's correctness and efficiency compared to existing alternatives on generative programs containing rejection sampling loops and discuss how to implement our method in a generic probabilistic programming framework.
We elaborate on using importance sampling for causal reasoning, in particular for counterfactual inference. We show how this can be implemented natively in probabilistic programming. By considering the structure of the counterfactual query, one can significantly optimise the inference process. We also consider design choices to enable further optimisations. We introduce MultiVerse, a probabilistic programming prototype engine for approximate causal reasoning. We provide experimental results and compare with Pyro, an existing probabilistic programming framework with some of causal reasoning tools.